To explain on that:
On rendering the NatTable asks its layers for the cell painter to use. Ususally this is the painter configured via NatTable configuration or specialized configuration by labels. In the special case of TreeLayer, the underlying painter is wrapped to be decorated with the tree image for expand/collapse. If you want to add padding, you have to wrap the created painter with a PaddingDecorator like shown above.

This is surely some part we have to look at when looking at the configuration of TreeLayer in general.

I wouldn't suggest to move back to 2.3.2 on SourceForge. There are a lot of bugfixes and improvements in the current head. And we are planning to do an official 0.9 release at the end of this month. So if this is a bug that can't be worked around, feel free to open a bug in bugzilla, so it can be fixed before release.

I'm not quite sure if the background rendering is processed correctly with your proposed solution. But if you don't configure different background color for your tree column, this shouldn't be an issue for you.